<div dir="ltr">Dear Tony,<div><br></div><div>I'm not wanting to create a full Bio-Linux installation in a container. As you say, that would be contrary to the purpose of containers. I'm more interested in creating a cut-down Bio-Linux-eqsue Docker image that has all the relevant command line tools installed for undertaking bioinformatics analyses, and access to the Bio-Linux 8 repos for installing additional tools as necessary.</div><div><br></div><div>Another way of doing this would be to simply use the ubuntu base image, add the Bio-Linux 8 repos, pin any GUI packages in apt with -1 priority, and install all command line packages as part of the Dockerfile configuration. Just trying to think of the easiest way to approach it.</div><div><br></div><div>I've followed Brad's work closely, so be interested to hear his take on this too.</div><div><br></div><div>Cheers,</div><div><br></div><div>Steve<br><div class="gmail_extra"><br><div class="gmail_quote">On 16 December 2014 at 12:00, <span dir="ltr"><<a href="mailto:bio-linux-request@nebclists.nerc.ac.uk" target="_blank">bio-linux-request@nebclists.nerc.ac.uk</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Message: 1<br>
Date: Mon, 15 Dec 2014 12:24:01 +0000<br>
From: Tony Travis <<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>><br>
To: <<a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a>><br>
Cc: Brad Chapman <<a href="mailto:chapmanb@50mail.com">chapmanb@50mail.com</a>><br>
Subject: Re: [Bio-Linux] BioLinux8 Dockerfile<br>
Message-ID: <<a href="mailto:548ED2E1.4050301@abdn.ac.uk">548ED2E1.4050301@abdn.ac.uk</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
On 14/12/14 14:40, Booth, Timothy G. wrote:<br>
> [...]<br>
> To answer your question, I'd suggest the following approach - take a<br>
> fresh Bio-Linux VM (ie. the .ova download) then remove the Gnome and<br>
> X libs packages. Lots of packages that depend on them will be<br>
> removed. Then you can diff the master package list from the upgrade<br>
> script and the packages you have left on the system to get your<br>
> blacklist. I'm sure there are other approaches but this is the one<br>
> that springs to mind.<br>
<br>
Hi, Tim and Steve.<br>
<br>
I think you're missing the point about Docker if you're trying to create<br>
a Bio-Linux container. Docker is a lightweight container that relies on<br>
the host OS to provide kernel services and system daemons.<br>
<br>
Bio-Linux is more appropriate as a host OS for Docker. I don't really<br>
see the point of trying to run a full Bio-linux in a Docker container<br>
because the overhead will be such that you might as well be using a VM.<br>
<br>
Docker is most useful for providing an OS independent environment for<br>
applications like e.g. GATK that have specific version dependencies that<br>
are quite difficult to reconcile with versions of programs that are<br>
installed on a particular host. Docker provides portability of an<br>
application between host and OS's by encapsulating these dependencies.<br>
<br>
Having said that, I'm currently trying to use Bio-Linux in a user-level<br>
"fakechroot" under 'Scientific' Linux (CentOS 6.3) on our HPC cluster<br>
because our out-sourced IT support company think Docker is too serious a<br>
security threat to be used on a 'production' server. I've pointed out<br>
that both AWS and Rackspace are offering Docker instances on their own<br>
cloud services 'securely'. I'm experimenting with Docker on my own PC.<br>
<br>
[I've CC'ed this to Brad to get his take on using Docker for Bio-Linux]<br>
<br>
Bye,<br>
<br>
Tony.<br></blockquote></div><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><a href="http://about.me/gawbul" style="margin:0px;padding:0px;border:0px;outline:0px;font-size:14px;vertical-align:baseline;color:rgb(43,130,173);text-decoration:none;line-height:18px" target="_blank"><font face="tahoma, sans-serif"></font><table border="0" cellpadding="0" cellspacing="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline;border-spacing:0px"><tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;vertical-align:baseline;height:30px"> </td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><td align="left" valign="top" style="padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:top;line-height:1"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:bold;font-style:inherit;font-size:18px;vertical-align:baseline;line-height:1;color:rgb(51,51,51)">Steve Moss</div><div style="margin:3px 0px 0px;padding:0px;border:0px;outline:0px;font-style:inherit;font-size:12px;vertical-align:baseline">about.me/gawbul</div></td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><td align="left" valign="top" style="padding:8px 0px 0px;border:0px;outline:0px;font-style:inherit;vertical-align:top;line-height:1"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline;text-align:right;background-color:rgb(197,208,224);height:4px"><img src="http://d13pix9kaak6wt.cloudfront.net/signature/colorbar.png" alt="Steve Moss on about.me" width="88" height="4" style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline;float:right;display:block"></div></td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;vertical-align:baseline;height:20px"> </td></tr></tbody></table></a></div></div>
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